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PRIDE Converter is available at http://code.google.com/p/pride-converter/
PRIDE Converter converts mass spectrometry data from most common data formats (MASCOT .dat file for example) into PRIDE XML.
(PRIDE XML is the file format used for submission to the publicly available PRIDE database).
It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service (OLS).
Below are the main steps to follow. For more details, see PRIDE Converter help which is accessible from each panel of the wizard.
Tips:
CV Term
to use, you can always Browse Ontology
Move Up
or Move Down
Select a File or a Folder
and select a Mascot .dat file (the choice of this Mascot file is not very important as we will only keep the header of the generated PRIDE XML file)Add Contact
Please Select a Contact
→ Create a New Contact…
(you can create as much as contacts as needed, at least one)If the experiment is part of a published manuscript it is highly recommended to include a reference to the paper.
Please Select a Sample Set
→ Create a New Sample Set…
(a sample set consists of one or multiple samples)Single sample
or Multiple Samples
tab (a Single Sample is most likely needed)Add Sample CV Term
to add a sampleChlamydomonas
, select the appropriate row in the Search Results
table, then click on Use Selected Term
.Please Select a Protocol
→ Create a New Protocol…
Add Protocol Step
(add as much protocol steps as needed)Ontology Lookup Service
enzyme digestion
as the Term Name
Search Results
table.Use Selected Term
Protocol Step
table. Depending on the CV Term, it may be possible to specify a value. You can enter, for ex., Trypsin
for the value of the Enzyme digestion
CV Term (just double-click on the Value
cell of this CV Term)2D Gel
or Other